same_ref {bigsnpr}

Determine reference divergence

Description

Determine reference divergence while accounting for strand flips. This does not remove ambiguous alleles.

Usage

same_ref(ref1, alt1, ref2, alt2)

Arguments

ref1

The reference alleles of the first dataset.

alt1

The alternative alleles of the first dataset.

ref2

The reference alleles of the second dataset.

alt2

The alternative alleles of the second dataset.

Value

A logical vector whether the references alleles are the same. Missing values can result from missing values in the inputs or from ambiguous matching (e.g. matching A/C and A/G).

See Also

snp_match()

Examples

same_ref(ref1 = c("A", "C", "T", "G", NA),
         alt1 = c("C", "T", "C", "A", "A"),
         ref2 = c("A", "C", "A", "A", "C"),
         alt2 = c("C", "G", "G", "G", "A"))